Genetics and Genomics Commons^™

Effects Of Time Of Transporting Prior To Sale Date On Selling Weight Of Weaned Steer Calves, L. M. Kovarik, Matt K. Luebbe, Joshua R. Benton, Galen E. Erickson, Richard J. Rasby

Department of Animal Science: Faculty Publications

Eighty-eight crossbred weaned steer calves (250 + 26 kg) were used to evaluate weight loss (shrink) when transported to a mock sale barn on differing days prior to sale. The calves were weaned 14 days and fed free choice grass hay and 0.9 kg of DDGS at UNL’s Dalbey-Halleck Research Unit. Two days before initiation of treatments all calves were fed grass hay ad libitum and initial BW were recorded on two consecutive days. Calves were assigned randomly to treatment as a completely randomized design. On d 2, 1d restricted and 1d ad libitum treatments were transported 150 km to …

Thirty-Seven Additional Microsatellite Loci In The Pacific Lion-Paw Scallop (Nodipecten Subnodosus) And Cross-Amplification In Other Pectinids, Jessica Lynn Petersen, Ana M. Ibarra, Bernie May

Department of Animal Science: Faculty Publications

We characterized 37 new microsatellite markers in the Pacific lion-paw scallop (Nodipecten subnodosus) and tested for cross-amplification in four other species. Genetic diversity was estimated using 24 individuals from the Lagoon Ojo de Liebre, B.C.S., Mexico. Allelic richness varied from 5 to 27 alleles per locus and the average expected heterozygosity was 0.76. Ten loci exhibited significant departure from Hardy–Weinberg equilibrium likely due to the presence of null alleles. Sixteen of these markers cross-amplified in closely related N. nodosus, while little or no amplification was observed in three Argopecten species.

Molecular Evolution Of Cytochrome B In High- And Low-Altitude Deer Mice (Genus Peromyscus), E. J. Gering, J. C. Opazo, Jay F. Storz

Jay F. Storz Publications

Patterns of amino-acid polymorphism in human mitochondrial genes have been interpreted as evidence for divergent selection among populations that inhabit climatically distinct environments. If similar patterns are mirrored in other broadly distributed mammalian species, then adaptive modifications of mitochondrial protein function may be detected in comparisons among locally adapted populations of a single wide-ranging species, or among closely related species that have adapted to different environments. Here, we test for evidence of positive selection on cytochrome b variation within and among species of the ecologically diverse rodent genus Peromyscus. We used likelihood-based comparisons of synonymous and nonsynonymous substitution rates to …

2009 Report : A Multi-Refuge Program To Evaluate The Effect Of Ungulate Browsing On Habitat, Richard B. Keigley, Jeffrey Warren, Wayne J. King

Aspen Bibliography

No abstract provided.

Supplementing Wet Distillers Grains Mixed With Low Quality Forage To Grazing Cow Calf Pairs, Brandon L. Nuttelman, William Griffin, T. J. Klopfenstein, Walter H. Schacht, Leslie Aaron Stalker, Jacqueline Musgrave, Jerry D. Volesky

Department of Animal Science: Faculty Publications

Two consecutive summer grazing studies were conducted to quantify the effect of supplementing cows with wet distillers grains (WDGS) mixed with low quality forage on 1) grazed forage intake and 2) cow and calf performance. During exp. 1, twenty-four three year old lactating cows rotationally grazed for 56 d and were assigned to one of three treatments: 1) the recommended stocking rate of 1.48 AUM/ha with no supplementation (CON1), 2) double the recommended stocking rate (2.96 AUM/ha) and supplemented 6.64 kg/hd daily of 45% grass hay and 55% WDGS (DM) to replace 50% of estimated total intake (SUP), and 3) …

Comparison Of Feeding Wet Distillers Grains In A Bunk Or On The Ground To Cattle Grazing Native Sandhills Winter Range, Jacqueline Musgrave, Leslie Aaron Stalker, Matthew C. Stockton, T. J. Klopfenstein

Department of Animal Science: Faculty Publications

Two-experiments determined the effects of feeding wet distillers grains with solubles (WDGS) either on the ground or in a bunk to cattle grazing native Sandhills winter range. In Experiment 1 (Exp. 1), 120 multiparous March-calving cows (536 ± 53.5 kg BW) were stratified by age and assigned to one of four treatments: WDGS fed on the ground, either three or six d/wk; or WDGS fed in a bunk either three or six d/wk. In Experiment 2 (Exp. 2), 63 March-born steer calves (201.2 ± 27.5 kg BW) were stratified by weight and assigned to one of two feeding treatments: WDGS …

Large-Scale Association Study For Structural Soundness And Leg Locomotion Traits In The Pig, Bin Fan, Suneel K. Onteru, Benny E. Mote, Timo Serenius, Kenneth J. Stalder, Max F. Rothschild

Department of Animal Science: Faculty Publications

Background: Identification and culling of replacement gilts with poor skeletal conformation and feet and leg (FL) unsoundness is an approach used to reduce sow culling and mortality rates in breeding stock. Few candidate genes related to soundness traits have been identified in the pig.

Methods: In this study, 2066 commercial females were scored for 17 traits describing body conformation and FL structure, and were used for association analyses. Genotyping of 121 SNPs derived from 95 genes was implemented using Sequenom's MassARRAY system.

Results: Based on the association results from single trait and principal components using mixed linear …

Age And Diet Affect Gene Expression Profile In Canine Skeletal Muscle, Ingmar S. Middelbos, Brittany M. Vester, Lisa K. Karr-Lilienthal, Lawrence B. Schook, Kelly S. Swanson

Department of Animal Science: Faculty Publications

We evaluated gene transcription in canine skeletal muscle (biceps femoris) using microarray analysis to identify effects of age and diet on gene expression. Twelve female beagles were used (six 1-year olds and six 12-year olds) and they were fed one of two experimental diets for 12 months. One diet contained primarily plant-based protein sources (PPB), whereas the second diet contained primarily animal-based protein sources (APB). Affymetrix GeneChip Canine Genome Arrays were used to hybridize extracted RNA. Age had the greatest effect on gene transcription (262 differentially expressed genes), whereas the effect of diet was relatively small (22 differentially expressed genes). …

Association And Haplotype Analyses Of Positional Candidate Genes In Five Genomic Regions Linked To Scrotal Hernia In Commercial Pig Lines, Zhi-Qiang Du, Xia Zhao, Natascha Vukasinovic, Fernanda Rodriguez, Archie C. Clutter, Max F. Rothschild

Department of Animal Science: Faculty Publications

Scrotal hernia in pigs is a complex trait likely affected by genetic and environmental factors. A large-scale association analysis of positional and functional candidate genes was conducted in four previously identified genomic regions linked to hernia susceptibility on Sus scrofa chromosomes 2 and 12, as well as the fifth region around 67 cM on chromosome 2, respectively. In total, 151 out of 416 SNPs discovered were genotyped successfully. Using a family-based analysis we found that four regions surrounding ELF5, KIF18A, COL23A1 on chromosome 2, and NPTX1 on chromosome 12, respectively, may contain the genetic variants important for the …

Effect Of Hydrogen Peroxide In The Scald Tank On The Microbial Count Of Pork Skin, A. S. De Mello Jr., R. O. Roca

Department of Animal Science: Faculty Publications

The objective of this study was to investigate the effect of hydrogen peroxide (H₂O₂) (50% v/v) on pork skin microbial populations. Forty-eight crossbred hogs were analyzed after dehairing and 30 during chilling. Three different concentrations of hydrogen peroxide were added to the scalding water (0.01, 0.05 and 0.1% of the total capacity of the scald tank). In treatment I no addition of H₂O₂ was applied while, in treatment II, H₂O₂ was added at 0 min and, in treatment III, it was added at 0, 30 and 60 min. Both treatments …

Development Of Pcr Assays To Detect And Characterise Salmonella Isolates From Cheese And Meat Products By Utilizing An Integrated Genomics Approach, Noelle Geraldine Mccarthy

Theses

Salmonella is an extremely important foodborne pathogen which is responsible for millions of cases of gastroenteritis annually. Salmonella outbreaks have been associated with numerous common food stuffs such as meat, dairy and seafood. Traditional culture based methods for the detection Salmonella are labourious and costly. Rapid detection and serovar identification would dramatically decrease the time required to identify Salmonella outbreaks and potential health risks.

In the US 99% of all Salmonella infections are caused by members of Salmonella enterica subspecies 1. Serovars within subspecies 1 can vary due to host specificity and pathogenicity. DNA sequencing projects have provided valuable genomic …

An Aspen Success Story : 2009 Aspen Monitoring Report, James L. Robertson

Aspen Bibliography

No abstract provided.

Proactive Procreation : Ethical Implications Of New Genetic Technologies For Parental Obligations To Future Offspring, L Syd M. Johnson

Legacy Theses & Dissertations (2009 - 2024)

This dissertation examines the ethical implications of recent genetic innovations, particularly preimplantation genetic diagnosis, for the obligations and duties of parents to future children. I critique common but uncompelling objections to the use of genetic information, diagnosis, and technology to influence the characteristics of future offspring, and conclude that genetic selection and enhancement are not different in kind or degree from other means of selection, direction, and enhancement that parents engage in to shape the lives of their children. Procreation is morally risky -- it risks imposing substantial burdens on persons who would not otherwise have to bear those burdens, …

Role Of Cyp2a5 In Drug Metabolism, Chemical Toxicity, And Maintenance Of Steroid Hormone Homeostasis : Insights From Studies On A Novel Cyp2a5-Null Mouse Model, Xin Zhou

Legacy Theses & Dissertations (2009 - 2024)

The central hypothesis is that CYP2A5 plays an important role in the metabolism of xenobiotic substrates, and in the toxicity induced by over-exposure to drugs, as well as in the metabolism of endogenous compounds and regulation of steroid hormone homeostasis. The specific aims are: 1) to generate and characterize a Cyp2a5-null mouse; 2) to determine the role of CYP2A5 in the systemic clearance of nicotine and cotinine; and 3) to explore the mechanisms underlying the resistance of the lateral nasal gland (LNG) of male Cyp2g1-null/Cyp2a5-low mouse and Cyp2a5-null mouse to acetaminophen (AP) toxicity.

An Rnai Screen Targeting The Protein Tyrosine Kinases Identifies Bruton's Tyrosine Kinase (Btk) As A Breast Cancer Cell Survival Factor, Cheryl Lynne Eifert

Legacy Theses & Dissertations (2009 - 2024)

The receptor protein tyrosine kinases (RPTKs) and the non- receptor protein tyrosine kinases (PTKs) are among the most commonly up-regulated genes found in all types of cancers. Although, a large body of data implicates a majority of tyrosine kinases (TKs) in cancer, few have been extensively evaluated for any potential therapeutic benefit in any of the many subtypes of breast cancer. We have used RNA interference (RNAi) to perform a large-scale loss-of-function analysis to facilitate the identification of individual factors necessary for the survival of an ErbB2 positive breast cancer cell line. We have found that 30% of the TKs …

Development Of A Gene Silencing Dna Vector Derived From A Broad Host Range Geminivirus, Edward M. Golenberg, D Noah Sather, Leandria C. Hancock, Kenneth J. Buckley, Natalie M. Villafranco, David M. Bisaro

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Gene silencing is proving to be a powerful tool for genetic, developmental, and physiological analyses. The use of viral induced gene silencing (VIGS) offers advantages to transgenic approaches as it can be potentially applied to non-model systems for which transgenic techniques are not readily available. However, many VIGS vectors are derived from Gemini viruses that have limited host ranges. We present a new, unipartite vector that is derived from a curtovirus that has a broad host range and will be amenable to use in many non-model systems.

Results

The construction of a gene silencing vector derived from the …

Primate Phylogenomics: Developing Numerous Nuclear Non-Coding, Non-Repetitive Markers For Ecological And Phylogenetic Applications And Analysis Of Evolutionary Rate Variation, Zuogang Peng, Navin Elango, Derek E. Wildman, Soojin V. Yi

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Genetic analyses are often limited by the availability of appropriate molecular markers. Markers from neutrally evolving genomic regions may be particularly useful for inferring evolutionary histories because they escape the constraints of natural selection. For the majority of taxa however, obtaining such markers is challenging. Advances in genomics have the potential to alleviate the shortage of neutral markers. Here we present a method to develop numerous markers from putatively neutral regions of primate genomes.

Results

We began with the available whole genome sequences of human, chimpanzee and macaque. Using computational methods, we identified a total of 280 potential …

Sexual Differentiation Of The Zebra Finch Song System: Potential Roles For Sex Chromosome Genes, Michelle L. Tomaszycki, Camilla Peabody, Kirstin Replogle, David F. Clayton, Robert J. Tempelman, Juli Wade

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Recent evidence suggests that some sex differences in brain and behavior might result from direct genetic effects, and not solely the result of the organizational effects of steroid hormones. The present study examined the potential role for sex-biased gene expression during development of sexually dimorphic singing behavior and associated song nuclei in juvenile zebra finches.

Results

A microarray screen revealed more than 2400 putative genes (with a false discovery rate less than 0.05) exhibiting sex differences in the telencephalon of developing zebra finches. Increased expression in males was confirmed in 12 of 20 by qPCR using cDNA from …

A Standardized Rna Isolation Protocol For Yam (Dioscorea Alata L) Cdna Library Construction, Satya S. Narina, Ali I. Mohamed, Robert Asiedu, H. D. Mignouna

Virginia Journal of Science

For the purpose of constructing yam cDNA libraries, attempts to isolate high quality RNA using several previously reported protocols were unsuccessful. Therefore a protocol was standardized for yam total RNA isolation by using guanidium buffer at the Department of Biology, Virginia State University. The RNA isolated using this standardized protocol was high in quality and led to successful good quality cDNA library construction and identification of functional ESTs in yam.

Estrogenic Compounds Downstream From Three Small Cities In Eastern Nebraska: Occurrence And Biological Effect, Marlo K. Sellin, Daniel D. Snow, Debbie L. Akerly, Alan S. Kolok

Biology Faculty Publications

Recent studies have detected estrogenic compounds in surface waters in North America and Europe. Furthermore, the presence of estrogenic compounds in surface waters has been attributed, in some cases, to the discharge of wastewater treatment plant (WWTP) effluent. The primary objective of the current study was to determine if WWTP effluent contributes estrogens to the surface waters of Nebraska. A second objective of this study was to determine if estrogens were found in concentrations sufficient enough to manifest feminizing effects on fish. These objectives were satisfied by deploying polar organic chemical integrative samplers (POCIS) and caged fathead minnows at eight …

Letter From The Dean, Lalit Verma

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

When Did The Ancestors Of Polynesia Begin To Migrate To Polynesia? The Mtdna Evidence, David Lesniewski

UNLV Theses, Dissertations, Professional Papers, and Capstones

The timing and nature of the migration of the ancestors of the Polynesian people is debated by two competing theories. The "Express Train" and "Slow Boat" theories assert that the migration of the Proto-Polynesian people began around 6,000 years before present (BP) or around 10,000 years BP respectively. Through the use of haplogroups and specific genetic mutations a direct relationship between the Proto-Polynesians and modern Polynesians was attempted to test which of these theories was correct. The ancient skeletal remains from the island of Borneo currently housed at UNLV were used in this study as their dates fall within both …

Comparing 2-Nt 3' Overhangs Against Blunt-Ended Sirnas: A Systems Biology Based Study, Preetam Ghosh, Robert Dullea, James E. Fischer, Tom G. Turi, Ronald W. Sarver, Chaoyang Zhang, Kalyan Basu, Sajal K. Das

Faculty Publications

In this study, we formulate a computational reaction model following a chemical kinetic theory approach to predict the binding rate constant for the siRNA-RISC complex formation reaction. The model allowed us to study the potency difference between 2-nt 3' overhangs against blunt-ended siRNA molecules in an RNA interference (RNAi) system. The rate constant predicted by this model was fed into a stochastic simulation of the RNAi system (using the Gillespie stochastic simulator) to study the overall potency effect. We observed that the stochasticity in the transcription/translation machinery has no observable effects in the RNAi pathway. Sustained gene silencing using siRNAs …

A Distribution-Free Convolution Model For Background Correction Of Oligonucleotide Microarray Data, Zhongxue Chen, Monnie Mcgee, Qingzhong Liu, Megan Kong, Youping Deng, Richard H. Scheuermann

Faculty Publications

Introduction

Affymetrix GeneChip^® high-density oligonucleotide arrays are widely used in biological and medical research because of production reproducibility, which facilitates the comparison of results between experiment runs. In order to obtain high-level classification and cluster analysis that can be trusted, it is important to perform various pre-processing steps on the probe-level data to control for variability in sample processing and array hybridization. Many proposed preprocessing methods are parametric, in that they assume that the background noise generated by microarray data is a random sample from a statistical distribution, typically a normal distribution. The quality of the final results depends …

High-Throughput Next-Generation Sequencing Technologies Foster New Cutting-Edge Computing Techniques In Bioinformatics, Mary Qu Yang, Brian D. Athey, Hamid R. Arabnia, Andrew H. Sung, Qingzhong Liu, Jack Y. Yang, Jinghe Mao, Youping Deng

Faculty Publications

The advent of high-throughput next generation sequencing technologies have fostered enormous potential applications of supercomputing techniques in genome sequencing, epi-genetics, metagenomics, personalized medicine, discovery of non-coding RNAs and protein-binding sites. To this end, the 2008 International Conference on Bioinformatics and Computational Biology (Biocomp) - 2008 World Congress on Computer Science, Computer Engineering and Applied Computing (Worldcomp) was designed to promote synergistic inter/multidisciplinary research and education in response to the current research trends and advances. The conference attracted more than two thousand scientists, medical doctors, engineers, professors and students gathered at Las Vegas, Nevada, USA during July 14-17 and received great …

An Ensemble Learning Approach To Reverse-Engineering Transcriptional Regulatory Networks From Time-Series Gene Expression Data, Jianhua Ruan, Youping Deng, Edward J. Perkins, Weixiong Zhang

Faculty Publications

Background

One of the most challenging tasks in the post-genomic era is to reconstruct the transcriptional regulatory networks. The goal is to reveal, for each gene that responds to a certain biological event, which transcription factors affect its expression, and how a set of transcription factors coordinate to accomplish temporal and spatial specific regulations.

Results

Here we propose a supervised machine learning approach to address these questions. We focus our study on the gene transcriptional regulation of the cell cycle in the budding yeast, thanks to the large amount of data available and relatively well-understood biology, although the main ideas …

Pervasive Hitchhiking At Coding And Regulatory Sites In Humans, James J. Cai, J. Michael Macpherson, Guy Sella, Dmitri A. Petrov

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Much effort and interest have focused on assessing the importance of natural selection, particularly positive natural selection, in shaping the human genome. Although scans for positive selection have identified candidate loci that may be associated with positive selection in humans, such scans do not indicate whether adaptation is frequent in general in humans. Studies based on the reasoning of the MacDonald–Kreitman test, which, in principle, can be used to evaluate the extent of positive selection, suggested that adaptation is detectable in the human genome but that it is less common than in Drosophila or Escherichia coli. Both positive and purifying …

Inheritance Of Shoulder Spotting In The Tetra, Hyphessobrycon Bentosi Characidae, Jack Frankel

Department of Biology Faculty Publications

The tetra (Hyphessobrycon bentosi) exhibits two phenotypes associated with shoulder spotting. Fish possess ei-ther a prominent black vertical spot located directly behind the operculum (H. b. bentosi,  bentosi  white  tip  tetra) or  lack  this spot (H. b. rosaceus, rosy tetra). Segregation patterns observed from the progenies of ten different crosses suggest that the  inheritance  of  these  phenotypes  is  controlled  by  two  autosomal  loci  acting  in  a complementary  fashion,  with  domi-nance at both loci required for the expression of the spotted phenotype. 

Inference, Orthology, And Inundation: Addressing Current Challenges In The Field Of Metagenomics, Gregory Detlev Alexander Vey

Theses and Dissertations (Comprehensive)

The vast increase in the number of sequenced genomes has irreversibly changed the landscape of the biological sciences and has spawned the current post-genomic era of research. Genomic data have illuminated many adaptation and survival strategies between species and their habitats. Moreover, the analysis of prokaryotic genomic sequences is indispensible for understanding the mechanisms of bacterial pathogens and for subsequently developing effective diagnostics, drugs, and vaccines. Computational strategies for the annotation of genomic sequences are driven by the inference of function from reference genomes. However, the effectiveness of such methods is bounded by the fractional diversity of known genomes. Although …

Construction Of A Transgene To Analyze The Function Of The 3’Utr Of The Hdc Gene On Spatial Expression Of Histidine Decarboxylase In Drosophila Melanogaster, Embriette Hyde, Martin G. Burg

Student Summer Scholars Manuscripts

Histamine has been shown to be an important neurotransmitter used in the nervous system of Drosophila melanogaster. Histidine decarboxylase (HDC) is the enzyme that catalyzes the synthesis of histamine. All genetic information necessary for Hdc gene expression has been shown to be present in a 9.4kb genomic DNA fragment. A previous study fused the 5'-UTR of Hdc to the gene encoding eGFP. Microscopic analysis of flies transformed with the pHdc-eGFP transgene showed a weak pattern of eGFP expression in the nervous system as compared to histamine localization, indicating that another genomic region may be necessary for robust Hdc expression. Studies …